RubyGems - ruby-ensembl-api - Versions diffs - 0.9.6 - Mend

ruby-ensembl-api 0.9.6

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (54) hide show

data/TUTORIAL.rdoc +623 -0
data/bin/ensembl +40 -0
data/lib/ensembl.rb +64 -0
data/lib/ensembl/core/activerecord.rb +1914 -0
data/lib/ensembl/core/collection.rb +60 -0
data/lib/ensembl/core/project.rb +264 -0
data/lib/ensembl/core/slice.rb +693 -0
data/lib/ensembl/core/transcript.rb +425 -0
data/lib/ensembl/core/transform.rb +97 -0
data/lib/ensembl/db_connection.rb +216 -0
data/lib/ensembl/variation/activerecord.rb +253 -0
data/lib/ensembl/variation/variation.rb +163 -0
data/test/unit/data/seq_c6qbl.fa +10 -0
data/test/unit/data/seq_cso19_coding.fa +16 -0
data/test/unit/data/seq_cso19_transcript.fa +28 -0
data/test/unit/data/seq_drd3_gene.fa +838 -0
data/test/unit/data/seq_drd3_transcript.fa +22 -0
data/test/unit/data/seq_drd4_transcript.fa +24 -0
data/test/unit/data/seq_forward_composite.fa +1669 -0
data/test/unit/data/seq_par_boundary.fa +169 -0
data/test/unit/data/seq_rnd3_transcript.fa +47 -0
data/test/unit/data/seq_ub2r1_coding.fa +13 -0
data/test/unit/data/seq_ub2r1_gene.fa +174 -0
data/test/unit/data/seq_ub2r1_transcript.fa +26 -0
data/test/unit/data/seq_y.fa +2 -0
data/test/unit/ensembl_genomes/test_collection.rb +51 -0
data/test/unit/ensembl_genomes/test_gene.rb +52 -0
data/test/unit/ensembl_genomes/test_slice.rb +71 -0
data/test/unit/ensembl_genomes/test_variation.rb +17 -0
data/test/unit/release_50/core/test_project.rb +215 -0
data/test/unit/release_50/core/test_project_human.rb +58 -0
data/test/unit/release_50/core/test_relationships.rb +66 -0
data/test/unit/release_50/core/test_sequence.rb +175 -0
data/test/unit/release_50/core/test_slice.rb +121 -0
data/test/unit/release_50/core/test_transcript.rb +108 -0
data/test/unit/release_50/core/test_transform.rb +223 -0
data/test/unit/release_50/variation/test_activerecord.rb +143 -0
data/test/unit/release_50/variation/test_variation.rb +84 -0
data/test/unit/release_53/core/test_gene.rb +66 -0
data/test/unit/release_53/core/test_project.rb +96 -0
data/test/unit/release_53/core/test_project_human.rb +65 -0
data/test/unit/release_53/core/test_slice.rb +47 -0
data/test/unit/release_53/core/test_transform.rb +63 -0
data/test/unit/release_53/variation/test_activerecord.rb +145 -0
data/test/unit/release_53/variation/test_variation.rb +71 -0
data/test/unit/release_56/core/test_gene.rb +66 -0
data/test/unit/release_56/core/test_project.rb +96 -0
data/test/unit/release_56/core/test_slice.rb +54 -0
data/test/unit/release_56/core/test_transform.rb +63 -0
data/test/unit/release_56/variation/test_activerecord.rb +142 -0
data/test/unit/release_56/variation/test_variation.rb +68 -0
data/test/unit/test_connection.rb +66 -0
data/test/unit/test_releases.rb +136 -0
metadata +128 -0

data/test/unit/data/seq_par_boundary.fa ADDED

@@ -0,0 +1,169 @@
+>Y dna:chromosome chromosome:NCBI36:Y:2705106:2715105:1
+TCCAAATGATGCTCTGCCATAAGAAGAAATTCACACCCTGAATAGCACAGCAGGATGCGA
+ATAGCAATGCCAGCCAAAGACATTGCAAACAAGCCGGTAAAACTAAGTGATTGTTAGCTG
+TTTAAAAAAATAATAATAACTGGTGTTAACAACAAAGTGAAACTTAACTTCTGAAGATGA
+GGCTACCTTCACAGAGAGGATAAGAAAGGAAGAACTGAGTAAAAGTAGTTAGATATTGCT
+GGATTTTGACATTTTAAGGTTAAGTGTTCCTGCTAAAAATAAAAATTGAACATATAACTC
+CTGAACTAGTGGATGAAAATGAAGAATGAAGAATAAAATTAAATACAAAAAAAATGAAGA
+GTAAAATTAAATACCAAAATTAGCCAAGTGTTGTGGTGAATGCCTGTAGTCCCAGCTACT
+CAGGAGGCTGAGGTGGGAGGATCACTTGAGCCCCAGAGGTGGAGGTTGCAGTGAGCTGAG
+ATTGCGCCACTGCACTTCCGCCTGGGTGGCAGAGCCAGGCTTTGTCTCAAAAATAAAAAA
+AAATAATAAATTAAAAACCTGAATACTAAATGGAAGTTAAGAAGGAAGGAATTAAAAAAG
+AAGAAAAGTAAAATAAAATAGTAGGAATAGTGAATCCTTAGTTATGTTAGATGTTCAGTG
+ATTTAATAAATCTGTAAAAAGACGGAGATGAGATGATGCAATTTAAAATGTTTCGGCTGG
+GCGCAGTGGCTCACGCCTGTAATCCCAGCACTGTAGGAAGCCGAGGCGGGTGGATCACGA
+GGTCAGGAGATCGAGACCATCCTGGCTAACACGGTGAAACCCCATCTCTACTAAAAATAC
+AAATAAAATGTTTCATGCTATTTACGAGAGAAGCATTTGCAACAAAATGCCAAAGAGAAG
+GTGAAAATAGCTGGAAAAAAAATGCGCAAAGCAAATAACCAATAGAAAGAAAGCCAAGTT
+GGGCTAGCAAAATCAGACAAAATAACCTTCGAGGTGCAAACAACTTTGAGGCCCAAATAG
+AGGTTCTTCCCACTAAAAGAATGATTCCCTGAATGATAATGGAATCTTGACCCAGCCTGC
+ACCTCAGGTTAAGTTAAAAGTGGAAATTTAAAGATCTAAGTGTGAGATTTTAAAAAGCAT
+TTCCCCAGAAATACCAGGATCTGTAGATGGAAATGTTATTAAGAATAAAGATGTGGAGCT
+GGGCGTGGTGGCTCACGCCTGTAATCCCAGAACTTTGGGAGGCTGAGACTGGCTGATTTC
+TTGAGCCCAGGAGTTTGAGACTAGCCTGGACAACATAGTGAGACCCCATCTTTACAAAAA
+AATTAAAAAAAATTAGTGGACATGGTGGCATGCACCTCTAGTCCCAGTTACTCAGGAGGC
+TGAGGTGGGAGGATCACCTGTGCCCAGGCTGAGGCTGCAGTGAGCCATGATCACGCCACT
+GCACTCCAGCCTGCGTGACAGAGCAAGACCCTGTCTCAAAAGAAAAGAAAAAAAAAGAAG
+AAAGAAATGAAAACCGTAGCTCAGAGACAGAGAAACTGAGCAATGCATAGGTTCAGAAGG
+GTTTGAAACAGACTGAATTGTGTCTTGGCATATGAGAGAGGTCGCAGCTATAAAACAATG
+AGAGAAGAAACCAAATTCCACATAGGCAGGACTGAGACAATTGGCTGTTCTTGTGGATGA
+TACGTGATCAAATCTCAACCTCATGCGATACTTTTTTTTTTTTTTTTGAGATGGAGTCTC
+GCTCTGTCACCCAGGCTGCAGTGCAGTGGTGTGATCTCACCTCCCCGCAAACTTCTCCTC
+CCGGGTTCAAGTAATTCTCGTGCCTCAGCTGGGACTACAGGCATGTGCCACCACGCCTGG
+CTAATTTTTGCATTTTTTTAGTAGAGACGGGGTTTCACCAAGTTGGCCAGGCTGGTCTCG
+AACTCCTGACCTCAGGTGATCTGTCCACCTCGGTGTCCCAAAGTGCTGGGATTACAGGTG
+TGAACCACCACACCCAGCCTCATGTAATACTTAAAAATGAACTACAGGTGGATTACAAAC
+CTGAATATAAAAGAAAACTTTTTTTTTTGAAAAATAGAGGGAAATGTCTTATAACCTCAG
+AGTTAGGAGGTTTTTCTTAGATACAATACAAAAAGCATAACCACGCCCATAGTCCCAGCT
+ACTCAGGAGGCTGAGGCATAAGAATCACTTGAGCTCGAGAGGTGGAGGTTGCAGTGAGCC
+GAGATCCTGCCATTGCACTCCAGCTGAGGCTACAGAGTGAGAGTATAAAAAAAAAAAAAA
+AAAAGCATAACCTTTAAAAATGGGTTAGCCTATGTCTACATTTAAATAATAATAATAATA
+ATAATGTTCCAACTTCAGGCTCTGAAAAAAGTCAAAAGATGAGCTGTCAACTAGAAGAGG
+CTCCTTACTGCTCATACCACCAGGGAAAGTTTAATATGCAAAATGCAGTCATCCTTCAGA
+ATTCATGGGGGATTAGTTTTAAGACGCCTTCTTCCCCGCAGACACCAAAATCCACAGCTG
+CTGAAGTCTCTGATATAAAACGTGCAGTACTTGCATATAATGCAAGTATATGTTCCTGTA
+TATTTTTATTTATTTATTTGGAGACAGAATCTCACTCTGTTGCCCAGGCTGGAGTGCAGT
+GGCGTGATCTTGGCTCACTGTAACCTCCACCTCCCGGGTTCAAGAGATTCTCCTGACTCA
+ACCTCCCAAGTAGCTGGGATTACAGGTATGCGCCACCACCCCCAGCTAATTTTTGTATTT
+TTGGTAGAGACGGGTTTTAACCATGTTGTCCAGGCTGGTTTCGAACTCCTGACCTCACAT
+AATCTGCCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGGATGAGCCACCGTGTCCAG
+CCTCTGGTATACTTTAAATTATCTCTAGGTTACTCATAACTCCTGATACGCTGTAAATGC
+TATGCAAATAGTTGTTATACTATATTATTTTTTATTTGTATTACTTTTTATTGGATTGCT
+ATATTTTATTTTTTGAAATATTTTCAATACAAGACTGGTTGGATCTATAGATGCAGAAAT
+TCTGGTTATAGAGCACAAACTGTGTATAGATAGCTCCTACCAAAACAGACGGATGGTGAA
+AAAAAGAAAAGAAAAGAAAAGAAAAAGAAAATGGAGGAGAGAGACTATGAGGCGACTAAA
+AGAAGAGGGATATGATCATTCCATTCGCTGACAAGAAAAATTCAAAGAAGAGGGAATTAT
+GCAATTGACCAGCTGATGTGTGTTAGAAATGCTCAGGGTCACACATATTCATTGAAAGCC
+AATTTAAGCCACTATTTAAATTTAAACCGATTTAAACAATTGGGCTTTTTTTTTTTTTTC
+TAAAAAAAAAAAAAAGTCAATTAGGCCAGGCGAGGTGGCTCACACCTGTCATCCCGGCAC
+TTTGGGAGGCCGAGGTGGGTGGATCACAAGGTCAGGAGTTTGAGACCAGCCTGGCCAACA
+TGGTGAAACCCTGTTTCTACTAAAAATACAAAAGTTAGCTGGGCATGGTGGTGTGTGCCT
+GAGGCTGTGAGACTGAGGCAGGAGAATCACTTGAACCCAGGAGGCGGAGGTTGCAGGGAG
+CGGAGATCATGCCACTGCACTCCAGCTTGGGCGACAGACCAAGACTCTGTCTCAAAAAAA
+AAAAAGAAGAAGTATATTGGTTCCGTCTGGAAAGGTGGAGCACTTGAAGCAAAGGCAGGA
+AGACTGGAAGCAGGGAGAGGGTTTTCAGGTCACAAACAGGTGAGAGACAAAACAGTTGCC
+TTCTTTTGAGTTTCTGATTAGCCTTTCCAAAGGAGGCGATCAGATACGAATCTGCCTCAG
+GGAGCAGAGGGGGGACTTTGAATAGAATGGGAGGCAGGTTGGCCCTAAGCAGTTCCCAGC
+TGGACTTTTCCCTTTAGCTTAGTGACTTGGGGGTCCCGAGATTTATGTTCCCTTCACAGT
+GTATGAGTGAGAGCACTTGGAAACTGAGAGTGGAAGTGTCGCAGGCCAGGTCTCACTAAC
+ACAGGCCCCCACAACACCTGTTTCAGTATTGACTGAGTGGTTAAATATTAAAAGCCAGTG
+CTGTTATACAAAGGCTGGAATGTAACAAAAGCCCACCGAGAGTTTTTCCCAGGACTTTCC
+CGGGCCTTAAAGCATGACAAAATAATGAATGAATTCTTAACAGGACCCATTTAGGATTAA
+ACAAGTTTTACTGGGGGTCTGCAGAAACTCCCCAGGCCTCCACAAACAAGTTTATTGGGG
+CTTTGAAGGAACTCTGCAAACCTCCTGGATTTAGCAGGAGACAACATGAGGGTAATCACC
+CCGGCACCTGGACCCATTAGATTAAGTCAATTTACTGAGGCTCCTGAGGAAGATCCTCAG
+GACTCAGACCTTAGTTATAGATTAAAAGAAGTTAAGGCCGGGCGCGGTGGCTCACGCCTG
+TAATCCCAGCACTTTGGGAGGCCAAGATGGGCGGATCACGAGGTCAGGAGATCGAGACCA
+TCTTGGCTAACACCGCGAAACCCCGTCTCTACTAAAAATACAAAAAAATCAGCCGGGCGT
+AGTGGCGGGCGCCTATAGTGCCAGCTACGCCGGAGGCTGAGGCAGGAGAGTGGCGTGAAC
+CCGGGAGGCGGCGCTTGCAGTGAGCTGAGATTGCGCCACTGCACTCCAGCCTGGGCGACA
+GAGCGAGACTCCGCCTCAAAAAAAAAAAAAAAAAAAAAAAAGTTAATCATTTATGTCGTT
+ACATAAATGGGCACTTACACATAGACGTATAGCTCAGAAGGTATATAAGCTCTATAAAAC
+TTTATCATTTTGAGTGGGTCTGGTAATATTATCTACATGCCTTCTCCCTGTAACCACTTG
+TAGAAATAAAAACTCTCTTCCTTCTCAGTTCATCTGCATCTCATTATTGGGCCACAAAAA
+AATAGCAGCCTGACCCTCAATTTGCTCAGGAAAGACAAGGGGACTTGGGAACACTCCTTA
+CACTTCAAAGAGAAGGCTCAAGGCCATTAAGAAAGACCTGTTGGGGTGCCATCCTTCCAT
+CTGGCTTAGTTAGTTCTTAAAAAGATTTACATATACCTCAAAAAACAGAGGGGAAAATAC
+TAGTTTTCTAAAGGTAGTACTCTAATGAAAAGTAGGAGGAAGGATTACTTTCTTACCTGA
+CAACAAGGAAAACTCAAATTACATAGATTTTAGACTTACAAAAATTTTCTGGACAGATAT
+GAAGAACATTATTAAACTAACAAACAGCAATCCAGAACTTTTTTTGTTGTTGTTTTTGCT
+AAACGTATTTGTAGTTCTGTTAATTTCCTTACTGTAATCTACCAACTTTATGTGATCTCT
+GTCTAAAAAGCAGAACTTTCTGGTCATTTCTAAAGAGCATAGAGATTTTAAGGAACATCA
+GCAATATTCAAATTTAAGAAAACTGATTATAACTTAGAAATTCTGAGGAAGAAGAGTAAT
+GAGGGGTAACTTGTTCTAGCAGAAAATCAAGTATATTTTTATAACCACTTTAATTATTTT
+AACTACATACCTTCATTCTGTGGTTAAAATTTAAGACACTAACAGTTCCAAATTTTGGTG
+AGCATGTATAGCAACGGAAAGCTCAGACATTGCTGTGGCAGTGTGAAATAGCACAAAAAC
+CCTGGAAAATTCTTGGAAAGGTACACACAAAATTAACTGAGCTGAAAATTTCACTCCTAG
+ATGTTGGCCCAGGTACATTAAAAACAGATGTCCACTTAGAGACTTGAGCTCAACTGTTGA
+TAGCAGCTTTATTAATAAAAGCCTCAAGCTCAAAATAGCCCAGTGTTCACCACCAACAGT
+GTACATAAACTGTGGTAAATTCATGCAAATTTCAACCTGAATGAAAGAAGCCAGATGCCC
+TTCAGAATACAGCTCCGTTGATATAAAGCCTTGAACTCAGCCGGGCGTGGTGGCTCACGC
+CTGTCATCCCAGCACTTTGAGAGGTCGAGGTGGGCAGATCACGAGGTCAGGAGATCGAGA
+CCATCCTGGCTAACACGGTGAAACCCTGGCTGTACTAAAAATACAAAAAATTATCCAGGC
+GTGGTGGCGGGCGCCTGTAGTCCCAGCTACTAGGGAGGCTGAGGCAGGAGAATGGCGTGA
+ACCGGGAGGCGGAGCTTGTGGTGAGCCTAGATTGGGCCACTGTACTCCATCCTGAGTGAC
+AGAGCAAGACTCTGTCTCAAAAAAAAAAAAAAAAGATCTCTCAATTGCATGATAGAAATC
+ATGCAATTGACAGAGGAATTGCAAAAGGGCACAGGAAATTTTAAGGGTTGAAGGAATGAT
+GTAAATAGCTTGTAACCTAGTTGGGGTGATAGTTACTCAGGCATATGCATTTGCCAAAGT
+TCATGCATCTATAAATAAAAGATCTGTGCACAATATCTCATGAAGATTTTTACTCTTGAC
+ATTATTACATAGTCCAATATGAAATAAAATATTAATTAAATTTCTTGAAATACTAGAACT
+CTGATAACTACCTTTTGTTTCTACACCTTGTAGAAACAAATCTTTGTGGAACAGATTTGG
+AACAAATATGGAAAATTAATGTATTTCACATCAGTAAAATCGTGACATTGGGAAAAACAT
+TACCCACTTCAATGCCTAATGAAATAATGTCTAATCAATCATGAATATCTACATTACTCT
+TCACTAAGATATTTTTTAGATGGAGCAATTACTTTCAGGTTAATAATAGCAAATATTTAG
+TTAATTCTTCACTAATGCTGATGTCTGTTCTAAGTATTTCTTTTTTTCTTTTCTTTTCTT
+TTTTTTTTTTTTTTTTTGTTGAGATGGAGTCTTGCTCTGTCGCCCAGGCTGGAGTGCAGT
+GGCGCCATCTTGGCTCACTGCAAGCTCCATCTACTGGATTCAAGCCCTCTCCTGCCTCAG
+CCTCCCAAGTAGCTGGGACTACAGGCGCCCGCCACCAAGCCTGGCTAATTTTTTGTATTT
+TTAGTAGAGACGGGGTTTCACCATGTTAGCTAGGATGATCTCAATCTCCTGACCTCGTGA
+TCCACCCACCTTGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACTGCTCCCAGCC
+TGTTCTAAGTATTTCTTATATACACTCACTTATTTAATGCTTGTGTACCTTAATTCATGT
+AGCCTTCACATCTCTTCATGGGTTGGTTTTATTAGTAAATAGCATTTCAACTAACAAAAT
+TATTACAGAATTGAAAAAACTGAGACTCAGACAGCGAAGTAAATTGTTCAAGCTCAAGCC
+TGTAAGTGGCACTCAAGTGAGCCAAAGCTGAAGGGTTTACCTTCCAGAGCCTGTGTTCTT
+TATTCAGTACCAAGCTCCCTCTTAATGTATTTTAAGTGTTGGCATTTTAAAATATAGCAA
+ACATCCATTGGCAGCCAAAGCACACTTGATACTTATAGTTAGAATTTGTTTGTTTATTGA
+TGTTTGTTTAAACATCACAAAAATACAAAAATGCTTCATTTCAGTAATTCCTAAGTAAAC
+CATACATAAAGTATCAATTCCTCTCCTGGGAGTGTGCTTCACAGAAATTCTTATAAATGT
+TCTCCATTGTACATGTATAAGAATGTATAAAAAAGCACTGTTTGTAATAATTGAAACCAG
+TAAGTGTCCATTCATTTGTCCAACAAAAATAGAATGAAATACGCACAACAATTTTTTCTT
+AAAAATTCTAGTTTGGGCAGCATATACACTAAAATTAGAATGGTATGGAGAAGAATAACA
+CTGTCCCTGGGCCAGGAGGGTATTCAAATGTGAAGTCTTTCATATTTTTGGGAGTAGAAT
+TGTGGCTACCCTCTAGTAGGGTCAGGTGAAGAGATGAGTATTGTTATTCAAAAATTATAA
+TATTTCATCTAGATAGAAGCAATTAGTTCAGATCTATTGTAAAGCATGTTGAATATAGGT
+AATAAGAATGTATTGTATGCTTGAAAATTGCTAAGAGAATACAATTTAAATGTTCCCAGT
+GCAAAAGGAAAGGGAAGTATATGAGGTAGTAGATACATTAGCTTGATTTAGTCTTTCCAA
+AATGTATACATGCATGATGTCATAATTTTTAATAATCTGAAAACCACCAAAATGTATTAA
+GCAAAAGAAGCTCCACATAATATTTTGTATTTATATTTATTCACATTGTTAAGGAAAAAT
+GGTATTCAGTGATACTTGTTCAAACTTGATAAGGAAGACTATTCACGACCAACAGCACAG
+CAATGAGGTCTTGCACTGGGGGAGAGATTGGCCTTAGCTCCACATACACAGCTGGGTAGG
+TGGGGATTTATAGCCAAGGAGCAGGGAGTAGGGTCAATGGATGGACAATCACTAAGAGAA
+GACATCATAGATAAGGAGGATTCTTGCTGAAGACAGGCTAGGCTGATCAGACATCACCTA
+GAGGGTGGTGGAGGATGAGAAACCTGATCAGATATTGAGGGTGATCGATCAAGTGTTGAG
+TGTGATCAGATATGCGGTGGGGGTACAGTCTGGCTAACCTGGCTTAGGAGAGTTCTTTGC
+CAAAACTGAGTTTGGCAAGGAAGTGCACAGGCGAGTCTAGGAGAAGGTTCAGAAACCTGA
+CTAAAGTTTGGTCAAACAGAGAATCTGTGTCAGAGGTTCAAGAAAAGGAAAATTAATGTA
+TGGTAATGAAGGTCAGAATGGGTGTTATTTTTGGGAGAGTGAAAAGAGTGGTTTTAAATA
+TTACAAAGTAGTTTTGAGTCAGTGTTTAAAAGGTAATGGGCAATATACAGTTCTCATTTG
+GCATAAAGCTCAGATTAAGTAATATTGTCTCTGGAATAAAGCTTTTTTTAAACCCTGAAC
+TTTGAGAAACATGACATCCATCTCTAATATACACTCTTTTAGTGTTTGAGTTTTATTATT
+TAAGGTAATGTCTCTGAAAAGTTTTGAAATATTGGAAAGCTGACTTTGATACATACCATT
+AATTTTGACTTTTGATTTATTTTTATTGTAGAAAAATTTATTTGTAATTTATACTTTAAA
+CTGTGGTTTACAGTTATTTGTAAACTTCTAGTTTCCTGCTTTAGCTTATGTGCAAATTTT
+ATGAAGTCTTGGCATTACATTTTTATTTAAATCCCATCAAATTAAACCAGTTGGGTCACC
+AGCCCCCGCCCTTCCATCTCCATAATCTGGGTAGTCGGCGTTCTCAACATTCCTGTTGAG
+AATGAAAATTCTGTATTTTTCATTCCACAGGCTTAAAAGTTAATAGGCCATGGAAACAAG
+TAGATTGCCATTTTAAAAGATAGTTTTCAGAAGAAAGGCAAAATGATAAGTTTCATAGAG
+ATACAAAAATGACAAGGAATTAAATATTTTGTTTTACCAGAGGCATTTTATAACTAGTTG
+AAAGGAAATGTCAACCGTTTGGATTTATATGGAGTAAAGGAACTGAATTGCAAGTGGAGG
+TAAAACTGGTTTTTTCCACAGCGTGAAGGGGAGAGAAAGAAACAAGTTTGATCCTGCTTA
+CATATCCATTCCTTAGTTACCTGCAATTTATAGACACGTACAAAGTAGCTGAAAGACCAA
+TGAATACACGGTCTAGAGAGGACTGCTTAACACGCTGCATATAGAAGTGTGATTTTTTTT
+GGTACAATTTTCAAGTGTGTTTCTCATTAGAGCATTTAAAGTAAGCCACAGTGTCCGTTT
+GTATCAAGTTAGTACTCTGACGGCCACAAACATAGGCAGGCTCACTTCTGGATGTCTTAT
+TTCTTTGCATGTTAATCGTGTTGACACAACTTGTCTTGAAATTAAGTTTAAAATGAAATA
+CCAGTAAAACTGAAATGAATAAGGCCTTTATTAGCCAGAGAAAAGAAAACAATATTGAAA
+CTAAACATAAGAAAGTGAGGGCTGTAAGTTATCGTAAAAAGGAGCATCTAGGTAGGTCTT
+TGTAGCCAATGTTACCCGATTGTCCTACAGCTTTGTCCAGTGGCTGTAGCGGTCCCGTTG
+CTGCGGTGAGCTGGCTGCGTTGATGGGCGGTAAGTGGCCT

data/test/unit/data/seq_rnd3_transcript.fa ADDED

@@ -0,0 +1,47 @@
+>ENSG00000115963|ENST00000263895
+CAGTCGGCTCGGAATTGGACTTGGGAGGCGCGGTGAGGAGTCAGGCTTAAAACTTGTTGG
+AGGGGAGTAACCAGCCTGCTCCTCTCGCTCTCCTCCTCGTCTGCGCCGCGTTTCAGAGAG
+AAAATTCCTGTTCCAAGAGAAAATAAGGCAACATCAATGAAGGAGAGAAGAGCCAGCCAG
+AAATTATCCAGCAAATCTATCATGGATCCTAATCAGAACGTGAAATGCAAGATAGTTGTG
+GTGGGAGACAGTCAGTGTGGAAAAACTGCGCTGCTCCATGTCTTCGCCAAGGACTGCTTC
+CCCGAGAATTACGTTCCTACAGTGTTTGAGAATTACACGGCCAGTTTTGAAATCGACACA
+CAAAGAATAGAGTTGAGCCTGTGGGACACTTCGGGTTCTCCTTACTATGACAATGTCCGC
+CCCCTCTCTTACCCTGATTCGGATGCTGTGCTGATTTGCTTTGACATCAGTAGACCAGAG
+ACCCTGGACAGTGTCCTCAAAAAGTGGAAAGGTGAAATCCAGGAATTTTGTCCAAATACC
+AAAATGCTCTTGGTCGGCTGCAAGTCTGATCTGCGGACAGATGTTAGTACATTAGTAGAG
+CTCTCCAATCACAGGCAGACGCCAGTGTCCTATGACCAGGGGGCAAATATGGCCAAACAG
+ATTGGAGCAGCTACTTATATCGAATGCTCAGCTTTACAGTCGGAAAATAGCGTCAGAGAC
+ATTTTTCACGTTGCCACCTTGGCATGTGTAAATAAGACAAATAAAAACGTTAAGCGGAAC
+AAATCACAGAGAGCCACAAAGCGGATTTCACACATGCCTAGCAGACCAGAACTCTCGGCA
+GTTGCTACGGACTTACGAAAGGACAAAGCGAAGAGCTGCACTGTGATGTGAATCTTTCAT
+TATCTTTAATGAAGACAAAGGAATCTAGTGTAAAAAACAACAGCAAACAAAAAGGTGAAG
+TCTAAATGAAGTGCACAGCCAAAGTCATGTATACCAGAGGCTTAGGAGGCGTTTGAGAGG
+ATACTCATCTTTTTGGAATCCTGACCTTAGGTTCGGCATGTAGACCAAGTGATGAGAAGT
+GAATACATGGAAGAGTTTTTAAGTGTGACTTGAAAAATATGCCAAAAAATGAGAGATACA
+AATGAGCTAGAGGAAGATGAGGGGGGATGCGAGTACCTCCAAGAAGAAAAATCACACTCT
+GAATGGTGCTTGCATTTTTGGGTTTTTTTTTTTTGTTATAATCTATTCATGGATCTCCAC
+TTTGATTTAATTTTTAAATGTTTTAATCTCCTTTACAAAAAGTATACGTTAATATACCGT
+CCTCAAGGGGGAACTGGCACTGTGACCTTAGCATTTAGTTTTCTAGAGGATGTGATCTAA
+TTTCTTTCTAGCTCATCATTAAAAAGGAAATTGTATCAGGACCCATGGGATATATCCAGA
+GGCAAACTTTATGAGGCTTTGAAATCTTGCCTTCCTGAAGATAGCTGAGTAGGATGGTTC
+TAAGGAAAGCCTTTGCAATCTTGCAAGATTTGTAGACCAGCACTACAAAGATCGCATAGA
+TCAAATAGGAAAAAAAATGTCGATTTTTATTCAGTCTGATGGTTCTGTTCTTCATTGTGA
+TTGTCATTAAAAAGTGGTAAATTGCTCAATGTAATATTTTTGTGCGCTGTTTAGAAGTTG
+TGTGATTTTTTGCCATCGTTGATAAAAATGCAAAGTCAAATAAAAGGTGTCTTGGTTTGA
+TGTCATAGAATGATCCAAGGAGAGAAAAAAGGTAGTTACTGTTTTCACCAGAAAAGGTAA
+TGAGTGAAGGAAAGAATAGTAGCAGAAAGCACAGTTTGTGAGTAAAGCTGTCTGGAATTA
+AGTTACCAAAAATACAAAGCAAAAGGACTATTATTTTGGGTTGAAGCTCCAAAACTGACA
+GCATCTGATAATCTGTTGGTTTATTTCACTTTTCATTAAATGAACATTGATGAGAGAAGA
+TGCCACTTACCCAAGCTTTAGAGAATCCCTAGTGGAAGATTATATGATAAACTTTCAGTC
+CTGACATAACACTAGGGCATTTCTAGAGTGTCATTGCTAAAACCTCACTGAACAGATGCA
+GCCAAGGTCTGTGTTCAGCACTTGGTCTCTGTTGTTACGTAAAATAATAAGCATTTAAAA
+TAGTTTACAGATATTTTTGACCAGTTCCTTTTAGAGATTCTTTCAGAGAAGAAACCAGAT
+CTGACCTGTTTATTGTTGGCGCTTGTTGAAAACGAGCTTTCTTTCCCATGATAGTGCTTC
+GTTTTTGAAGTGTTGAAGCTGTGCTCCCCTTAAATCGTGGCAGGAGAGATTAAGGTAATT
+ACAACACTCAGTTCTATGTCTTACAAGCACTTTGTCTTGTCTCTGCAAGAAAATTCGATT
+CCAGTCATTTCCCATAAAATACAGACATTTTACCAACATAATATGCTTTGATTGATGCAG
+CATTATGCTTTGGGCAGTATTACAAAATAGCTGGCGAGTGCTTTCTGTATTTAAATATTG
+TAAAAAGAAAATAAGTTATAACTGTTATAAAGCAGAACTTTTGTTGCATTTTTTAAACTG
+TTGAAGTCACTGTGTATGTTTGTTTGGTCAATGTTTCCGCAGTATTTATTAAAACATACT
+TTTTTTTTCTTCAAATAAAAAAGTAACCATGTCTTTGTCTAAA

data/test/unit/data/seq_ub2r1_coding.fa ADDED

@@ -0,0 +1,13 @@
+>UB2R1_coding
+ATGGCTCGGCCGCTAGTGCCCAGCTCGCAGAAGGCGCTGCTGCTGGAGCTCAAGGGGCTG
+CAGGAAGAGCCGGTCGAGGGATTCCGCGTGACACTGGTGGACGAGGGCGATCTATACAAC
+TGGGAGGTGGCCATCTTCGGGCCCCCCAACACCTACTACGAGGGCGGCTACTTCAAGGCG
+CGCCTCAAGTTCCCCATCGACTACCCATACTCTCCACCAGCCTTTCGGTTCCTGACCAAG
+ATGTGGCACCCTAACATCTACGAGACGGGGGACGTGTGTATCTCCATCCTCCACCCGCCG
+GTGGACGACCCCCAGAGCGGGGAGCTGCCCTCAGAGAGGTGGAACCCCACGCAGAACGTC
+AGGACCATTCTCCTGAGTGTGATCTCCCTCCTGAACGAGCCCAACACCTTCTCGCCCGCA
+AACGTGGACGCCTCCGTGATGTACAGGAAGTGGAAAGAGAGCAAGGGGAAGGATCGGGAG
+TACACAGACATCATCCGGAAGCAGGTCCTGGGGACCAAGGTGGACGCGGAGCGTGACGGC
+GTGAAGGTGCCCACCACGCTGGCCGAGTACTGCGTGAAGACCAAGGCGCCGGCGCCCGAC
+GAGGGCTCAGACCTCTTCTACGACGACTACTACGAGGACGGCGAGGTGGAGGAGGAGGCC
+GACAGCTGCTTCGGGGACGATGAGGATGACTCTGGCACGGAGGAGTCCTGA

data/test/unit/data/seq_ub2r1_gene.fa ADDED

@@ -0,0 +1,174 @@
+>UB2R1_gene
+GGCAAGCGCCGGTGGGGCGGCGGCGCCAGAGCTGCTGGAGCGCTCGGGGTCCCCGGGCGG
+CGGCGGCGGCGCAGAGGAGGAGGCAGGCGGCGGCCCCGGTGGCTCCCCCCCGGACGGTGC
+GCGGCCCGGCCCGTCTCGCGAACTCGCGGTGGTCGCGCGGCCCCGCGCTGCTCCGACCCC
+GGGCCCCTCCGCCGCCGCCATGGCTCGGCCGCTAGTGCCCAGCTCGCAGAAGGCGCTGCT
+GCTGGAGCTCAAGGGGCTGCAGGAAGAGCCGGTCGAGGGATTCCGCGTGACACTGGTGGA
+CGAGGGCGATCTATACAACTGGGAGGTGGCCATCTTCGGGCCCCCCAACACCTACTACGA
+GGGCGGCTACTTCAAGGTGAGCGCGGCGACCCCCGCCCGGGTCCCGGAGCCCACGAGCGA
+CCTCGGGCGCCGGGAACCAGCTCCCTGCCCCGCGGTCCTAGCGCTGTTGCTGGGCGGGCC
+CCGAAGCCTCCTGGCTTGGGCTCGTTTCCCTTCTATGGCCACGTTCCCCCACCCAGCTCT
+GCCCGGCCCCCTCCTCGGACCGTCTCGGGGACCTTCAGCCTCTGCTGCAGTCCTCGAAAA
+TCCCCAGTTCCCTTCAAGGCATCGTCCGGTCCCCTGTTAGGCTCTTGGCCCCCGGAGGGG
+TGGCCGGGGGCCCTCCCTGTAGCATCTGGGCGTGGGGCTCTTGCCCACCTCCTCCTTGGC
+GGGGGCTGGACCCCGGCTGCCTCCCCCTCCGCCCCTGCGAGAAAGAGGGAGCGGAGCCCA
+GGCCGCGCCGGCCTTTCAGCTGCCCTCCCCGCCCTCCCCGGAGGAGACAAAGAGGCCCCC
+CCAGACCCCGTAGCTGCTATTGTTGGGGAGCTGGGCCCGTGAGCGGGGGAGCGAGGCCAG
+CCTGGGGGTGGCTGGCGCGGCCACTCGCTCAGTCTCCAACAAAGGCCCGGATGAGCCTTG
+GCAGCCAGGACCCGCCTGGAAAGCGGCCACCCTTGCCAGTAGCAGCCGGCCAGGCGCCCT
+GGGCTCCATCCCCTGCTTTATGTAACCTGCGCCCTCGGGAAGGCCGAAGTAGGGGCGTGC
+CTCCCACCTGCTCCCTGCAGCTCTCTCCAGGCCTCCCGGCTCGGGCCCGCGTCCCGGACC
+CCGACCTCAGAAGCTCCGGGCTCGCTCATCCCAGCTGGTCTTGGCCTTTCTCAGAGTCCA
+CTGAACAGGTGGCTTCTTGGGACCCAAACCCCGAGTTCTGGGCCGTTTCTTCTGCCCTCT
+GGCGGTTTAATTCCAAGCAGTTTCTGGATGTTTTTGTTGTTGTTGGGAGCGGGGAGGCTG
+TTTCTGTCTCATGTGAAAAGGACTCAGGCCAAAACCAGGGCAGTTTTCTTGATCTCACGA
+TCCAGACGTGACCTTTGACTTCTTTTAGCGTTCAGGGACCTCGTTCTTGGGGCCAGAGGG
+ACAAAGCGAGGGGCCCTGTGTGAGCGGTGGGGAACGAGCACCCTGTCCAGGAATCTCCCC
+CTCCCACCGTCACTTCCTGCCAAGAGCCTGGACACGACACGACACTGCAGGGCCCGGCCC
+GCTCTGCCCCGGCCAGCTGCGGGCGTGGGGCCGAGGGACCGATGCCTCCCGCACGATATG
+TGTCTGCTCTCCGAGCTAATTAGTGTCTGAACCGCACCCGCTCAGCGGCTGTGAGGGCAG
+CAGCCTGGTCTGCTGGGGGCGATTCCTGAGCAGAGAGTGGGACGCCCGTGGGTTCTGCAT
+CTGGAATCCTGCGTCCCCACACAGGGAACAGAGTTTGGGTCTCGAGGTTGCCAAATGGTT
+TTAGCAGCTCCTCCGCCAGCCCCTTCTGTCTGCTTGGGGGAGCAGCTGGCTGAGGAGCCG
+CAGCCCCACCTCGAAGCCAGGCCTGTGAGGCGGCTGCTGTTCTGGAAGGAGGGGATGGGG
+GTTTCTGGCTGCTGTGCCCACCAGACCGGTTGCCAGGGATTGTGGGCAGAGCTTCCTGGG
+CCAGCATTAGGGGATAATCCGGTTTTCCGGATTTCCCAGGGAGGGGGCCTCTAGACATCT
+GCCACAGGGTCAGTCCTCAGAAGCCAGTGTTGAGACGGGGGTGCTGCCACCCACGAGGAC
+TCTCCCTTCCCGCTGTGCCTGGGAGGGAGTTGGGGGAGCGTGGAAATACAGAACCTGCTG
+AGTGCCCAGGGCCGCTGCTGCCCAGCCACTGCCTGCAGCTGCTGTTCCTTCAGGAGCCAA
+AGTGAGCCCTGGGGCAGGGGCCGCCAGAGAGAGCCCTCCACAGCCGACTTGCTGTCTGCC
+CTTGGCAGGGCGCTTTCCTTTTCTGAGCCTGGGTTTGCTCCGGGGAAAAGACATTCTTAG
+AGGTGCCCAAAATAAGAGGCTCATTGGGACTTGGTGGGGTTTGGTACAGATGAGGCCTTG
+GCTGTTGTCAAGGATTGCCGCCTGAAACCCAGCACCAGGCTTGGGGGGCCTGAAGTCTTG
+GGGAACCGCAGGACAGTTCTGAGACTGAAGTTCCAGCCTTGCTCTGTGGCCGCGGCCAAG
+TCACTTGCCTTACGGGGCACCAGTGAGTTCCCTGTCAAACAGAGGACACCCCCCAAGACA
+CCCCGCGTGCCCTCCCTGTCCAGGAGGGGCCCGTCCACGATCCAAGACCCCCAAAGTGCC
+CTGCCTGTCCGGGAGGGGCCTCGCCCACAATCCAAGACCCCCGAGTACCCTCCCTGTCCA
+GACCTCGCCCACGATCCAAGACCCCCTGAGTGCCCTCCCTGTCCAGACCTCACCCACGAT
+CCAAGACCCCCTGAGTGCCCTCCCTGTCCAGACCTCGCCCACAATCCAAGACCCCCGAGT
+ACCCTCCCTGTCAAGGCCTCGCCCACGATCCAAGACCCCCGAGTGCCCGCCCTGTCCAGA
+CCTCGCCCACGATCCAAGACCCCCGAGTGCCCTCCCTGTCCAGACCTCGCCCACGATCCA
+AGACCCCCGAGTGCCCTCCCTGTCCAGACCTCGCCCACGATCCAAGACCCCCGAGTGCCC
+TCCCTGTCCAGACCTCGCCCACGATCCAAGACCCCCGAGTGCCCTCCCTGTCCAGACCTC
+GCCCATGATCCAAGACCCCCGAGTGCCCTCCCTGTCCAGACCTCGCCCACGATCCAAGAC
+CCCCTGAGTGCCCTCCCTGTCCAGACCTCGCCCACGATCCAAGACCCCCTGAGTGCCCTC
+CCTGTCCAGGCTTCCACCACGATCGCTCTGGGGGTGCTGCTCTCGTGCCTTGGAGTGCTG
+AGTGCCACCAGGACCCCTGACCCAGACAACCTCTGTGTCTGGCACTGGGGCCCAGCAGGA
+AAACAGTGAGGCTTCCTTGTTTACCTGCTGTGGCCCAGGAGGGCCGTGGGTGGCATCACG
+CCCCAGGCTGCAGGCCAGACAGCTCTGTCACCTGGCACGTGGCTTCAGGCCTCCCTCTGT
+GGCCGTCCTTGCCAGCAGATCTGGACCTCCAGGGCCTGGGTGACCACAGGGGGCGATGCT
+GACAGGGAAGGAGTCCTGCCAGGTTTCTGTGACCTATGGGTCTGCCTGCCTGACCCCCCA
+AGACCGGACACCTGAGGGCAGACGGCCATACTGACTCATCCCCTCCCACGGCCTGGGCCA
+GGGCAGGTGTCACAAGTGTTTGCTAACTGAGCAATCATCTGTGCTAACCCTCCCCACACC
+CTGGCTGCCAAGGCCCTGGAGGTGCAGCCCTGGTCCTGGGCTTCAGCTCCATCCAAGGGG
+AGCCTGGAGCCCCTGCCAGTCCATTCTGTCTGCTGGTGGGTGCCCCTGGCCTGGGTCCCA
+TATGCCTGACCTGGGCTGCCACGGGCCTGGAGCCACGCGGGCAGCCAGTGCCCACGTTCC
+CCAGCAGTTGTGCTGGGCCGGGTCCCGGCCACCTGGACTGTGTAGGAGCTGGGATCAGCT
+CGGGTGACTCAGAAAAGGCTTCAGGCAGCCTTCTGGGGACTTGACCCCAGGCCTGTGAGA
+GTCCCTGCCTTGGGCAGGATACGGTGTCCCTCACACACACCCTCAGGCACCAGCACTGGG
+AGTGGGATGGCCTTGGGCACCTTGTGAGCTGGGGCAGGTCTTGGGGCTGGGCTGGACTGA
+GCCACCTGCCTTCTGCCCCTGCAGGCGCGCCTCAAGTTCCCCATCGACTACCCATACTCT
+CCACCAGCCTTTCGGTTCCTGACCAAGATGTGGCACCCTAACATCTACGAGGTGAGCGCG
+GCCCCCACGGGCCTCAAGTCCTCATCCTCCGGGACCCAGGGTGCTGGGAGCCTCACGTCC
+TCATCCTTCCGGGACCCGGGGCGCTGGGAGCCTCACGTCCTCGTCCTCCGGGACCCGGGG
+CGCTGGGAGCCTCACGTCCTCGTCCTTCCGGGACCCGAGGCGCTGGGAGCCTCATGTCCT
+CGTCCTTCCGGGACCCGGGGCGCTGGGAGCCTCACGTCCTCGTCCTCCACGTCCTCATCC
+TCCGGGACCTGGGGCACTGGGAGCCCGTGCTGACCTCTGACCTGTTCTGACCTGTCTTCT
+TCTTGTGCAGACGGGGGACGTGTGTATCTCCATCCTCCACCCGCCGGTGGACGACCCCCA
+GAGCGGGGAGCTGCCCTCAGAGAGGTGGAACCCCACGCAGAACGTCAGGTAAGCCGGCCC
+AACCCCCTGTGTCCACCCAGAACATCAGGTAGGCCGGGCTCCGTCCCGTATCCACCCAGA
+CCATCAGGTAGGCCGGGCTCCCCCACAGGCTGTGGCGCCAAGGCCTGATTCGGGACCTGC
+CAGCTGGCGGTCCTGGGCCTCGCTGTACCTGCACGGTAGGTGCTTTCACGGGGCCTGCGG
+CACCGTGTGTCGGTGCAGACTCCCACCAGGACCCCAGGCCGGCCCCACCGTCTGGAACCA
+CCTAGAGGTGTCCCGCCATCCTCAGTCCTGGGGCCTTCTCCTTACCCAGCCGTCTCTGGG
+TTGGTCACCTCGTGCCACGTGTGCCGCCTGGGCCTCGTCCCCAGGTACAAGCACTGGGCC
+GTGTTGCCCGTGTGTCCTGGAGTGTAGTCTAGGCAGGACGTGCGGGTGTGAGGGCAGCCC
+CGGGTCTGACGGAGGGGTCTGCACCTTGCTGCCCTCCCTGGTCTTGGCGTGGGAGGGAGG
+AGACTGATGCAGGTCCAGCCCCTGCTGTTCTGGGGGCCTGAGACAGAAGCAGAGGCCATG
+AGGCCAGGTGAAGGTCACCTGCTGGGTGGGTCCAGGCGTCCCCGTGACCCTCAGGGCCAG
+AGAAGAGCCGGAAGGCTGGGGTGCCCCGGGCCGCCCCACTCCGACCCACTCTCCCCACAG
+GACCATTCTCCTGAGTGTGATCTCCCTCCTGAACGAGCCCAACACCTTCTCGCCCGCAAA
+CGTGGACGCCTCCGTGATGTACAGGAAGTGGAAAGAGAGCAAGGGGAAGGATCGGGAGTA
+CACAGACATCATCCGGTGAGGGCGGGCGGGGGCGTCACGGGAGGAGAGACTCAGATCCGG
+CCTGCACCCCGGCCCCTGGTCCCACGGCCGCCCAGCCCCACCTTCCTGGTGAGGGTGGCG
+GAGCTTCCTGGTGCCCATTTACAGGGTGCCAGTCACAGATGGAGGCCGGGCCGAGTGGCG
+GAGGGTCCAGCCAGGTTCAAGCCCAGCTTCTTGCCCCTTTTCCTCTTTTTTTTTGTTTGA
+GACAGAGTCTCTCTCTGTCACCCAGGCTGGAGTGCAGTGGCGCGATCTCGGCTCACTGCA
+AGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCTGGGACTA
+CAGGCGCCCGTCACCACGCCCGGCTAATTTTTTGTATTTTTAGTAGAGACGGGGTTTCAG
+CGTGTTAGCCAGGATGGTCTCGATCTCCTGACCTCGTGATCCATCTGCCTCGGCCTCCCA
+AAGTGCAGGGATTACAGGCGTGAGCCACCGCGGCCGGCCTTTTTTTTTTTTTTTTTTTTT
+GGAGACAGAGTTATACTCTCTTGCCTAGGCTGCAGTGCAGTGGTGCGATCTCGGCTCACT
+GCAGCCTCCACTACTCGGGTTGGAGCAGTTCTCCCCCTTCATCCTGCCAAGCAGCTGGGA
+TTACAGGTGCCCACTACCACGCCGAGCTAATTTTTGTAATTTTTAGTAGAGGTGGGATTT
+CACCATCTTAGCCAGGCTGGTCTCAAACTCCTGACCTCAGGTGATCCACCCGCCTCGGCC
+TCCCAAAGTGCTGGGATGACAGGCGTGAGCCACTGCACCTGGCCTGGTGGTTAGTGTTTT
+CATAGATTCTTCCAGGCTTTTCAGTTTAACGCATGTCTGTGCTTTAATGAAGAAATGGGG
+TCGTGCTGTGTGTGCCCAGTGACTGACTGTTAGGGAACATGTGTCTGTGCCTTAATGAAG
+AAATGGGGTCGTGCTGTGTGTGCCCAGTGACTGACTGTTAGGGAACATGTGTCTGTGCTT
+TAATGAAAAAATGGGGTCGTGCTGTGTGTGCCCAGTGACTGACTGTTAGTCAGGGGTGTT
+GGCCTTACTCATGTCTGGAGTGCGTCCCTGCAGGCTCTTGGCCTGGTGAGCTCTGGGTAC
+AGCTGTGCAGTCGCCTACCGGCGCCTTCTGTACCTGCAGTCCACTTAGCTTGCGTGGCTG
+TGTGTGGTGACCCACGGCTCTCCCTCTCCTCCCATCGCCCTCATGCCCCAGAGCTGAGCC
+CCACAGCCCCTTCTCTTGGGTGCCTGTGTTCACATGAATGTGTAAACACGTGCGTGTCTG
+TGTACAAAGACAAGGCTTTCTTTACGGGTTGACGGCCTTAATGGTTCCTGCTCTTCCTGT
+TACATAGAGGCCCTTCCTATCCATTTTTTTTTTTTCTCAGAGTGATATTGCATAGATTTC
+CTCACAGAGGCCTCACCTATTTTTGTTGGTATTTTGTATAAACAGAATCTTAAAAACAAC
+TTTTAAAATATTGCACACATAATGCATGTGTCTTCCTCGCCCCAGGACCCAGGAGCATCC
+AGGGCACCTTCCATCCTGCACTCGCTGGTACCTGGTGTCGTGGGGTCATCTCGGGGCAGC
+ATCCTGGTGCTGGGCGGTCTCGGCTCTGAGCAGCCATGGTGGGCGGGCCCCGTGCGGCCT
+CCTGGGAAGTGGCCTGCAAGCACCTGCTGGCCTCTGGAGGTCACAGGGTAGCTGCCCTGG
+CCGTCCCTCTGGTGCAGATGTCCTCGGTGGCCCCGGTCCGGTCGTGTCACCTGGCCCAGG
+TGGCTGGCTCCTTGGCCCGGTTCTTCCCGGCCACCTCCCTGAGGCACCACCTCCTTGAGA
+TCCCAGCACAGAAATAAAAGCCACACTATTTTTATCCCTCAAAACTCCCTGTGGGCCAAC
+ACACATGTGCCATGTGGACTCTGCTGTGGTCGCCGTTTCTGCCTGTTTTTTCATCTGTGT
+GCGTGTTGGCCTCGTGGCAGCCCAAGTCCCGCTGAGCTGTGTCGGGCAGGCTGCCGTGGA
+GCCCGGCTTGGTCAGGGATGTTGGTCTTGCTGAACAGGACCTCCAGACCGTCCTCCAGCT
+CATGCTGGCGGTGTGCCGGCGGCACCTCCACGGTGCAGGTCAGTTCCCACCCTGGCCCTC
+CCCTGCGTCTCCCCACAGCCGCCACCTCTGCGGTGCCGTCCCCGGGGCACCGTCACCCCC
+CCAGCCCGTCCACCCTGGCCCTCCCCTGCGTCTCCCCACTGCTGCCACCCGTGCAGTGCC
+GTCCCCGGGGCACTGTCAGTCACCCCCCCAGCCCATCGGAGAGCTTGGAAAGCAAAGCTT
+GGCGTCCGCTGGGTCCCGCCACCCAGGGACGTCCCTGAGGCCAGACGCCTGCCCTCCACG
+CGTCATGCATCCCCATAAAAAGCACTGGGCTTGTGGGCTGGGCTTGGGGCTGTCTGTCTG
+CTCCCTGGTGCCCTCCCATGCGGGCACTGTGGGACCCGCACACCCTGGTAGCAGCCAGCC
+CCAGAGCCCAGAGCCGTGCCTGGTCGGTGATAGGGGCTCGAGCCCATTGCCTGCGGCTGC
+AGCCTCGTTCCTGTTTTCTGTCAAATGGGGTCAGCGTGCCGCCTGGCCCTGCTGTGCCAC
+CCCCGGAAGCCCCTTTGCTTCCAGTCCTGGGGGGACATTCTTGACGCGTGTCCTGGAGGT
+GGAGCCGGGGGCAGGTTCCTCGTAGGTCCTGGTGTGCGCGGTGCAGCCCCTCATAGGGCC
+GGGTGTACACGGTGCCCTCCAGGAAGTTTGAGCTAACTTGTCCTCCCTTCCTGCCAGAGG
+CTGGGATGGCCAGGCCCCCCAGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCAGG
+TTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCCACGTTTAGAATCCGGAGGCCGGGGT
+GGCCAGGCCCCCCAGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCCACGTTTAGA
+ATCCGGAGGCCGGGGTGGCCAGGCCCCCCGGGTTTAGAATCCGGAGGCCGGGGTGGCCAG
+GCCCCCCGGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCCGGGTTTAGAATCCGG
+AGGCCGGGGTGGCCAGGCCCCCCGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCC
+GGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCCGGGTTTAGAATCCGGAGGCCGG
+GGTGGCCAGGCCCCCCGGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCCGGGTTT
+AGAATCCGGAGGCCGGGGTGGCCAGGCCCCCCGGGTTTAGAATCCGGAGGCCGGGGTGGC
+CAGGCCCCCCGGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCCGGGTTTAGAATC
+CGGAGGCCGGGGTGGCCAGGCCCCCCGGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCC
+CCCCGGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCCGGGTTTAGAATCCGGAGG
+CCGGGGTGGCCAGGCCCCCCACGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCGGG
+TTTAGAATCCGGAGGCTGGGATGGCCAGGCCCCCGGGTTTAGAATCCAGAGGCTGGGATG
+GCCAGGCCCCCCGGTTTAGAATCCGGAGGCCGGGGTGGCCAGGCCCCCGGGTTTAGAATC
+CTGCTGAGGCCACGGAGAGGCTCAGGCCGTTTTTGCGTTTCCCATCTCACCTGTGCTGGT
+TCCCGTCTCCAGGGATGGTCCTGCCTCCTGTCCTTGGGCCCTCCCAGCTGCTTCCTTTGC
+TCCTGCGCTGAGGAAGGCTTTTGCCCCCCAGTGGGGCAGCATGGGCCCTCCCTGTTGCCG
+GCATCGTTATTTTCTCCCAGCTCCTGATGGGTCCCTTGGGTTGTGCTTCGGGGCGGGGCA
+GGCGGGTGTGACTGCACTGCGCCCGTCCAGCCTCCCACCCGCACCTCCTGCCCTTCCCGA
+GCCCCCTCCTCTGTCATTTCTCCCCCTGGAGTTCCTCACGCACAGGGCTTTGTCCTAAGT
+GGTCGCCACACGCCGTTTTAAGAGAAACCTGAGCGTTGGGGTGAGCGTCGGACCTGGGGG
+AGGGGGGCCGGGCAGGGGCCGAGTCCAGGCACGTGGGTGGCGCCCTCACCCACCCTGTCC
+CCCCAGGAAGCAGGTCCTGGGGACCAAGGTGGACGCGGAGCGTGACGGCGTGAAGGTGCC
+CACCACGCTGGCCGAGTACTGCGTGAAGACCAAGGCGCCGGCGCCCGACGAGGGCTCAGA
+CCTCTTCTACGACGACTACTACGAGGACGGCGAGGTGGAGGAGGAGGCCGACAGCTGCTT
+CGGGGACGATGAGGATGACTCTGGCACGGAGGAGTCCTGACACCACCAGAATAAACTTGC
+CGAGTTTACCTCACTAGGGCCGGACCCGTGGCTCCTTAGACGACAGACTACCTCACGGAG
+GTTTTGTGCTGGTCCCCGTCTCCTCTGGTTGTTTCGTTTTGGCTTTTTCTCCCTCCCCAT
+GTCTGTTCTGGGTTTTCACGTGCTTCAGAGAAGAGGGGCTGCCCCACCGCCACTCACGTC
+ACTCGGGGCTCGGTGGACGGGCCCAGGGTGGGAGCGGCCGGCCCACCTGTCCCCTCGGGA
+GGGGAGCTGAGCCCGACTTCTACCGGGGTCCCCCAGCTTCCGGACTGGCCGCACCCCGGA
+GGAGCCACGGGGGCGCTGCTGGGAACGTGGGCGGGGGGCCGTTTCCTGACACTACCAGCC
+TGGGAGGCCCAGGTGTAGCGGTCCGAGGGGCCCGGTCCTGCCTGTCAGCTCCAGGTCCTG
+GAGCCACGTCCAGCACAGAGTGGACGGATTCACCGTGGCCGACTCTTTTCCCTGCTTTGG
+TTTGTTTGAAATCTAAATAAAACTACTTTATG

data/test/unit/data/seq_ub2r1_transcript.fa ADDED

@@ -0,0 +1,26 @@
+>UB2R1_transcript
+GGCAAGCGCCGGTGGGGCGGCGGCGCCAGAGCTGCTGGAGCGCTCGGGGTCCCCGGGCGG
+CGGCGGCGGCGCAGAGGAGGAGGCAGGCGGCGGCCCCGGTGGCTCCCCCCCGGACGGTGC
+GCGGCCCGGCCCGTCTCGCGAACTCGCGGTGGTCGCGCGGCCCCGCGCTGCTCCGACCCC
+GGGCCCCTCCGCCGCCGCCATGGCTCGGCCGCTAGTGCCCAGCTCGCAGAAGGCGCTGCT
+GCTGGAGCTCAAGGGGCTGCAGGAAGAGCCGGTCGAGGGATTCCGCGTGACACTGGTGGA
+CGAGGGCGATCTATACAACTGGGAGGTGGCCATCTTCGGGCCCCCCAACACCTACTACGA
+GGGCGGCTACTTCAAGGCGCGCCTCAAGTTCCCCATCGACTACCCATACTCTCCACCAGC
+CTTTCGGTTCCTGACCAAGATGTGGCACCCTAACATCTACGAGACGGGGGACGTGTGTAT
+CTCCATCCTCCACCCGCCGGTGGACGACCCCCAGAGCGGGGAGCTGCCCTCAGAGAGGTG
+GAACCCCACGCAGAACGTCAGGACCATTCTCCTGAGTGTGATCTCCCTCCTGAACGAGCC
+CAACACCTTCTCGCCCGCAAACGTGGACGCCTCCGTGATGTACAGGAAGTGGAAAGAGAG
+CAAGGGGAAGGATCGGGAGTACACAGACATCATCCGGAAGCAGGTCCTGGGGACCAAGGT
+GGACGCGGAGCGTGACGGCGTGAAGGTGCCCACCACGCTGGCCGAGTACTGCGTGAAGAC
+CAAGGCGCCGGCGCCCGACGAGGGCTCAGACCTCTTCTACGACGACTACTACGAGGACGG
+CGAGGTGGAGGAGGAGGCCGACAGCTGCTTCGGGGACGATGAGGATGACTCTGGCACGGA
+GGAGTCCTGACACCACCAGAATAAACTTGCCGAGTTTACCTCACTAGGGCCGGACCCGTG
+GCTCCTTAGACGACAGACTACCTCACGGAGGTTTTGTGCTGGTCCCCGTCTCCTCTGGTT
+GTTTCGTTTTGGCTTTTTCTCCCTCCCCATGTCTGTTCTGGGTTTTCACGTGCTTCAGAG
+AAGAGGGGCTGCCCCACCGCCACTCACGTCACTCGGGGCTCGGTGGACGGGCCCAGGGTG
+GGAGCGGCCGGCCCACCTGTCCCCTCGGGAGGGGAGCTGAGCCCGACTTCTACCGGGGTC
+CCCCAGCTTCCGGACTGGCCGCACCCCGGAGGAGCCACGGGGGCGCTGCTGGGAACGTGG
+GCGGGGGGCCGTTTCCTGACACTACCAGCCTGGGAGGCCCAGGTGTAGCGGTCCGAGGGG
+CCCGGTCCTGCCTGTCAGCTCCAGGTCCTGGAGCCACGTCCAGCACAGAGTGGACGGATT
+CACCGTGGCCGACTCTTTTCCCTGCTTTGGTTTGTTTGAAATCTAAATAAAACTACTTTA
+TG

data/test/unit/data/seq_y.fa ADDED

	@@ -0,0 +1,2 @@
1	+ >Y dna:chromosome chromosome:NCBI36:Y:2709497:2709542:1
2	+ TAGTTATAGATTAAAAGAAGTTAAGGCCGGGCGCGGTGGCTCACGC

data/test/unit/ensembl_genomes/test_collection.rb ADDED

@@ -0,0 +1,51 @@
+#
+# = test/unit/release_53/ensembl_genomes/test_collection.rb - Unit test for Ensembl::Core
+#
+# Copyright::   Copyright (C) 2009
+#               Francesco Strozzi <francesco.strozzi@gmail.com>
+# License::     Ruby's
+#
+# $Id:
+require 'pathname'
+libpath = Pathname.new(File.join(File.dirname(__FILE__), ['..'] * 4, 'lib')).cleanpath.to_s
+$:.unshift(libpath) unless $:.include?(libpath)
+require 'test/unit'
+require 'lib/ensembl'
+include Ensembl::Core
+class TestCollection < Test::Unit::TestCase
+  def teardown
+    DBConnection.remove_connection
+  end
+  def test_check_collection
+    DBConnection.ensemblgenomes_connect('bacillus_collection',3)
+    assert_equal(true,Collection.check)
+    DBConnection.connect('homo_sapiens',56)
+    assert_equal(false,Collection.check)
+  end
+  def test_check_species
+    DBConnection.ensemblgenomes_connect('bacillus_collection',3)
+    assert_equal(["Bacillus subtilis","Bacillus amyloliquefaciens","Bacillus anthracis Ames","Bacillus anthracis Ames ancestor","Bacillus anthracis Sterne","Bacillus cereus ATCC 10987","Bacillus cereus ATCC 14579","Bacillus cereus NVH 391-98","Bacillus cereus ZK","Bacillus clausii","Bacillus halodurans","Bacillus licheniformis Goettingen","Bacillus licheniformis Novozymes","Bacillus pumilus SAFR-032","Bacillus thuringiensis Al Hakam","Bacillus thuringiensis konkukian 97-27","Bacillus weihenstephanensis","Bacillus cereus AH820","Bacillus cereus AH187","Bacillus cereus Q1","Bacillus cereus G9842","Bacillus cereus B4264"],Collection.species)
+  end
+  def test_get_species_id
+    DBConnection.ensemblgenomes_connect('bacillus_collection',3)
+    assert_equal(9,Collection.get_species_id("Bacillus cereus ZK"))
+    assert_nil(Collection.get_species_id("Dummy specie"))
+  end
+  def test_connection_with_a_species
+    assert_nothing_raised do
+      DBConnection.ensemblgenomes_connect('Bacillus_licheniformis_Goettingen',3)
+    end
+    assert_equal('bacillus licheniformis goettingen', Ensembl::SESSION.collection_species)
+  end
+end